Multiple sequence alignment - TraesCS3A01G032500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G032500 chr3A 100.000 3087 0 0 1 3087 18817917 18821003 0.000000e+00 5701.0
1 TraesCS3A01G032500 chr3A 100.000 2089 0 0 1 2089 19267063 19264975 0.000000e+00 3858.0
2 TraesCS3A01G032500 chr3A 87.981 624 60 8 2479 3087 745905249 745905872 0.000000e+00 723.0
3 TraesCS3A01G032500 chr3A 95.844 409 11 2 1692 2095 19269652 19269245 0.000000e+00 656.0
4 TraesCS3A01G032500 chr3A 93.182 44 3 0 2090 2133 369397018 369397061 7.150000e-07 65.8
5 TraesCS3A01G032500 chr3D 94.588 1164 60 2 924 2087 17698205 17699365 0.000000e+00 1797.0
6 TraesCS3A01G032500 chr3D 85.175 1113 142 13 1000 2093 17343131 17342023 0.000000e+00 1120.0
7 TraesCS3A01G032500 chr3D 88.784 633 42 12 2477 3085 587475261 587475888 0.000000e+00 749.0
8 TraesCS3A01G032500 chr3D 91.844 282 16 5 563 843 17698087 17697812 1.340000e-103 387.0
9 TraesCS3A01G032500 chr6D 84.349 1099 158 10 1005 2093 417752071 417750977 0.000000e+00 1064.0
10 TraesCS3A01G032500 chr6D 82.684 1103 152 25 1003 2087 417775857 417776938 0.000000e+00 942.0
11 TraesCS3A01G032500 chr6D 88.718 195 21 1 2479 2672 426931385 426931191 1.430000e-58 237.0
12 TraesCS3A01G032500 chr6B 83.244 1116 163 13 992 2087 626643906 626645017 0.000000e+00 1003.0
13 TraesCS3A01G032500 chr6B 88.517 627 46 14 2476 3085 2806721 2806104 0.000000e+00 736.0
14 TraesCS3A01G032500 chr6B 88.320 625 50 11 2478 3085 309686036 309686654 0.000000e+00 728.0
15 TraesCS3A01G032500 chr6B 84.026 770 109 9 1334 2093 626489330 626488565 0.000000e+00 728.0
16 TraesCS3A01G032500 chr6A 83.258 1099 170 11 1005 2093 560192872 560191778 0.000000e+00 998.0
17 TraesCS3A01G032500 chr6A 81.125 1102 159 22 1003 2087 560444263 560445332 0.000000e+00 837.0
18 TraesCS3A01G032500 chr6A 87.967 615 51 10 2490 3087 473572138 473571530 0.000000e+00 704.0
19 TraesCS3A01G032500 chr6A 91.414 198 15 2 2476 2672 593456818 593456622 1.410000e-68 270.0
20 TraesCS3A01G032500 chr6A 84.848 231 33 2 1003 1232 560489042 560489271 6.660000e-57 231.0
21 TraesCS3A01G032500 chr1D 89.524 630 48 7 2476 3087 101104528 101105157 0.000000e+00 782.0
22 TraesCS3A01G032500 chr1D 86.240 625 54 16 2478 3085 476403354 476402745 0.000000e+00 649.0
23 TraesCS3A01G032500 chr1D 92.683 41 3 0 2093 2133 339110983 339110943 3.320000e-05 60.2
24 TraesCS3A01G032500 chr2A 89.677 620 47 7 2483 3087 25097431 25096814 0.000000e+00 774.0
25 TraesCS3A01G032500 chr2A 86.076 474 38 14 2483 2931 749798365 749797895 4.630000e-133 484.0
26 TraesCS3A01G032500 chr1A 88.052 611 55 11 2493 3087 440148309 440147701 0.000000e+00 708.0
27 TraesCS3A01G032500 chr1A 86.230 610 64 7 2476 3085 549125016 549124427 0.000000e+00 643.0
28 TraesCS3A01G032500 chr1B 87.640 623 57 10 2476 3079 16777388 16778009 0.000000e+00 706.0
29 TraesCS3A01G032500 chr3B 86.872 617 52 18 2485 3085 825637423 825636820 0.000000e+00 664.0
30 TraesCS3A01G032500 chrUn 85.191 628 48 13 2494 3085 319124385 319123767 1.220000e-168 603.0
31 TraesCS3A01G032500 chrUn 86.243 567 42 12 2494 3033 375367803 375367246 1.600000e-162 582.0
32 TraesCS3A01G032500 chrUn 83.830 235 19 9 2151 2384 38150196 38150412 4.040000e-49 206.0
33 TraesCS3A01G032500 chr4A 83.943 629 66 16 2476 3076 646515391 646516012 1.240000e-158 569.0
34 TraesCS3A01G032500 chr2D 84.326 319 23 7 2476 2770 586913376 586913691 1.400000e-73 287.0
35 TraesCS3A01G032500 chr5D 95.349 43 2 0 2091 2133 526842864 526842906 5.520000e-08 69.4
36 TraesCS3A01G032500 chr5B 97.500 40 1 0 2096 2135 486482443 486482482 5.520000e-08 69.4
37 TraesCS3A01G032500 chr5B 93.023 43 3 0 2091 2133 662602725 662602767 2.570000e-06 63.9
38 TraesCS3A01G032500 chr7B 93.023 43 3 0 2091 2133 405065534 405065576 2.570000e-06 63.9
39 TraesCS3A01G032500 chr7A 93.023 43 3 0 2093 2135 464911524 464911482 2.570000e-06 63.9
40 TraesCS3A01G032500 chr7D 91.111 45 4 0 2090 2134 607100181 607100137 9.240000e-06 62.1
41 TraesCS3A01G032500 chr5A 92.857 42 3 0 2093 2134 476653230 476653189 9.240000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G032500 chr3A 18817917 18821003 3086 False 5701 5701 100.000 1 3087 1 chr3A.!!$F1 3086
1 TraesCS3A01G032500 chr3A 19264975 19269652 4677 True 2257 3858 97.922 1 2095 2 chr3A.!!$R1 2094
2 TraesCS3A01G032500 chr3A 745905249 745905872 623 False 723 723 87.981 2479 3087 1 chr3A.!!$F3 608
3 TraesCS3A01G032500 chr3D 17698205 17699365 1160 False 1797 1797 94.588 924 2087 1 chr3D.!!$F1 1163
4 TraesCS3A01G032500 chr3D 17342023 17343131 1108 True 1120 1120 85.175 1000 2093 1 chr3D.!!$R1 1093
5 TraesCS3A01G032500 chr3D 587475261 587475888 627 False 749 749 88.784 2477 3085 1 chr3D.!!$F2 608
6 TraesCS3A01G032500 chr6D 417750977 417752071 1094 True 1064 1064 84.349 1005 2093 1 chr6D.!!$R1 1088
7 TraesCS3A01G032500 chr6D 417775857 417776938 1081 False 942 942 82.684 1003 2087 1 chr6D.!!$F1 1084
8 TraesCS3A01G032500 chr6B 626643906 626645017 1111 False 1003 1003 83.244 992 2087 1 chr6B.!!$F2 1095
9 TraesCS3A01G032500 chr6B 2806104 2806721 617 True 736 736 88.517 2476 3085 1 chr6B.!!$R1 609
10 TraesCS3A01G032500 chr6B 309686036 309686654 618 False 728 728 88.320 2478 3085 1 chr6B.!!$F1 607
11 TraesCS3A01G032500 chr6B 626488565 626489330 765 True 728 728 84.026 1334 2093 1 chr6B.!!$R2 759
12 TraesCS3A01G032500 chr6A 560191778 560192872 1094 True 998 998 83.258 1005 2093 1 chr6A.!!$R2 1088
13 TraesCS3A01G032500 chr6A 560444263 560445332 1069 False 837 837 81.125 1003 2087 1 chr6A.!!$F1 1084
14 TraesCS3A01G032500 chr6A 473571530 473572138 608 True 704 704 87.967 2490 3087 1 chr6A.!!$R1 597
15 TraesCS3A01G032500 chr1D 101104528 101105157 629 False 782 782 89.524 2476 3087 1 chr1D.!!$F1 611
16 TraesCS3A01G032500 chr1D 476402745 476403354 609 True 649 649 86.240 2478 3085 1 chr1D.!!$R2 607
17 TraesCS3A01G032500 chr2A 25096814 25097431 617 True 774 774 89.677 2483 3087 1 chr2A.!!$R1 604
18 TraesCS3A01G032500 chr1A 440147701 440148309 608 True 708 708 88.052 2493 3087 1 chr1A.!!$R1 594
19 TraesCS3A01G032500 chr1A 549124427 549125016 589 True 643 643 86.230 2476 3085 1 chr1A.!!$R2 609
20 TraesCS3A01G032500 chr1B 16777388 16778009 621 False 706 706 87.640 2476 3079 1 chr1B.!!$F1 603
21 TraesCS3A01G032500 chr3B 825636820 825637423 603 True 664 664 86.872 2485 3085 1 chr3B.!!$R1 600
22 TraesCS3A01G032500 chrUn 319123767 319124385 618 True 603 603 85.191 2494 3085 1 chrUn.!!$R1 591
23 TraesCS3A01G032500 chrUn 375367246 375367803 557 True 582 582 86.243 2494 3033 1 chrUn.!!$R2 539
24 TraesCS3A01G032500 chr4A 646515391 646516012 621 False 569 569 83.943 2476 3076 1 chr4A.!!$F1 600

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 4711 0.457035 GGGGCGTTCGTGATGTACTA 59.543 55.0 0.0 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3068 5756 1.069765 AATACCGGCAGATCAGCGG 59.93 57.895 15.68 15.68 35.37 5.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2093 4711 0.457035 GGGGCGTTCGTGATGTACTA 59.543 55.000 0.00 0.00 0.00 1.82
2094 4712 1.553308 GGGCGTTCGTGATGTACTAC 58.447 55.000 0.00 0.00 0.00 2.73
2095 4713 1.133790 GGGCGTTCGTGATGTACTACT 59.866 52.381 0.00 0.00 0.00 2.57
2096 4714 2.416431 GGGCGTTCGTGATGTACTACTT 60.416 50.000 0.00 0.00 0.00 2.24
2097 4715 2.850647 GGCGTTCGTGATGTACTACTTC 59.149 50.000 0.00 0.00 0.00 3.01
2098 4716 2.850647 GCGTTCGTGATGTACTACTTCC 59.149 50.000 0.00 0.00 0.00 3.46
2099 4717 3.427233 GCGTTCGTGATGTACTACTTCCT 60.427 47.826 0.00 0.00 0.00 3.36
2100 4718 4.730657 CGTTCGTGATGTACTACTTCCTT 58.269 43.478 0.00 0.00 0.00 3.36
2101 4719 5.159209 CGTTCGTGATGTACTACTTCCTTT 58.841 41.667 0.00 0.00 0.00 3.11
2102 4720 5.060569 CGTTCGTGATGTACTACTTCCTTTG 59.939 44.000 0.00 0.00 0.00 2.77
2103 4721 5.717078 TCGTGATGTACTACTTCCTTTGT 57.283 39.130 0.00 0.00 0.00 2.83
2104 4722 5.706916 TCGTGATGTACTACTTCCTTTGTC 58.293 41.667 0.00 0.00 0.00 3.18
2105 4723 4.863131 CGTGATGTACTACTTCCTTTGTCC 59.137 45.833 0.00 0.00 0.00 4.02
2106 4724 5.176592 GTGATGTACTACTTCCTTTGTCCC 58.823 45.833 0.00 0.00 0.00 4.46
2107 4725 4.841813 TGATGTACTACTTCCTTTGTCCCA 59.158 41.667 0.00 0.00 0.00 4.37
2108 4726 5.487488 TGATGTACTACTTCCTTTGTCCCAT 59.513 40.000 0.00 0.00 0.00 4.00
2109 4727 6.670464 TGATGTACTACTTCCTTTGTCCCATA 59.330 38.462 0.00 0.00 0.00 2.74
2110 4728 6.938698 TGTACTACTTCCTTTGTCCCATAA 57.061 37.500 0.00 0.00 0.00 1.90
2111 4729 7.504926 TGTACTACTTCCTTTGTCCCATAAT 57.495 36.000 0.00 0.00 0.00 1.28
2112 4730 8.612486 TGTACTACTTCCTTTGTCCCATAATA 57.388 34.615 0.00 0.00 0.00 0.98
2113 4731 9.220906 TGTACTACTTCCTTTGTCCCATAATAT 57.779 33.333 0.00 0.00 0.00 1.28
2147 4765 7.406031 TTTTACACTAGTATGAGACAGAGGG 57.594 40.000 0.00 0.00 0.00 4.30
2148 4766 4.864483 ACACTAGTATGAGACAGAGGGA 57.136 45.455 0.00 0.00 0.00 4.20
2149 4767 4.787551 ACACTAGTATGAGACAGAGGGAG 58.212 47.826 0.00 0.00 0.00 4.30
2150 4768 4.228666 ACACTAGTATGAGACAGAGGGAGT 59.771 45.833 0.00 0.00 0.00 3.85
2151 4769 5.429109 ACACTAGTATGAGACAGAGGGAGTA 59.571 44.000 0.00 0.00 0.00 2.59
2152 4770 5.761234 CACTAGTATGAGACAGAGGGAGTAC 59.239 48.000 0.00 0.00 0.00 2.73
2153 4771 5.668535 ACTAGTATGAGACAGAGGGAGTACT 59.331 44.000 0.00 0.00 0.00 2.73
2154 4772 4.787551 AGTATGAGACAGAGGGAGTACTG 58.212 47.826 0.00 0.00 39.65 2.74
2156 4774 4.864483 ATGAGACAGAGGGAGTACTGTA 57.136 45.455 0.00 0.00 45.54 2.74
2157 4775 4.652679 TGAGACAGAGGGAGTACTGTAA 57.347 45.455 0.00 0.00 45.54 2.41
2158 4776 4.994282 TGAGACAGAGGGAGTACTGTAAA 58.006 43.478 0.00 0.00 45.54 2.01
2159 4777 5.391256 TGAGACAGAGGGAGTACTGTAAAA 58.609 41.667 0.00 0.00 45.54 1.52
2160 4778 5.243283 TGAGACAGAGGGAGTACTGTAAAAC 59.757 44.000 0.00 0.00 45.54 2.43
2161 4779 5.145564 AGACAGAGGGAGTACTGTAAAACA 58.854 41.667 0.00 0.00 45.54 2.83
2162 4780 5.601313 AGACAGAGGGAGTACTGTAAAACAA 59.399 40.000 0.00 0.00 45.54 2.83
2163 4781 6.270231 AGACAGAGGGAGTACTGTAAAACAAT 59.730 38.462 0.00 0.00 45.54 2.71
2164 4782 6.231211 ACAGAGGGAGTACTGTAAAACAATG 58.769 40.000 0.00 0.00 44.06 2.82
2165 4783 5.122396 CAGAGGGAGTACTGTAAAACAATGC 59.878 44.000 0.00 0.00 0.00 3.56
2166 4784 4.980573 AGGGAGTACTGTAAAACAATGCA 58.019 39.130 0.00 0.00 0.00 3.96
2167 4785 5.381757 AGGGAGTACTGTAAAACAATGCAA 58.618 37.500 0.00 0.00 0.00 4.08
2168 4786 6.010219 AGGGAGTACTGTAAAACAATGCAAT 58.990 36.000 0.00 0.00 0.00 3.56
2169 4787 6.151144 AGGGAGTACTGTAAAACAATGCAATC 59.849 38.462 0.00 0.00 0.00 2.67
2170 4788 6.151144 GGGAGTACTGTAAAACAATGCAATCT 59.849 38.462 0.00 0.00 0.00 2.40
2171 4789 7.309194 GGGAGTACTGTAAAACAATGCAATCTT 60.309 37.037 0.00 0.00 0.00 2.40
2172 4790 8.082242 GGAGTACTGTAAAACAATGCAATCTTT 58.918 33.333 0.00 0.00 0.00 2.52
2173 4791 9.463443 GAGTACTGTAAAACAATGCAATCTTTT 57.537 29.630 0.00 0.00 0.00 2.27
2174 4792 9.463443 AGTACTGTAAAACAATGCAATCTTTTC 57.537 29.630 0.00 0.00 0.00 2.29
2175 4793 7.713764 ACTGTAAAACAATGCAATCTTTTCC 57.286 32.000 0.00 0.00 0.00 3.13
2176 4794 7.271511 ACTGTAAAACAATGCAATCTTTTCCA 58.728 30.769 0.00 0.00 0.00 3.53
2177 4795 7.224557 ACTGTAAAACAATGCAATCTTTTCCAC 59.775 33.333 0.00 0.00 0.00 4.02
2178 4796 7.044181 TGTAAAACAATGCAATCTTTTCCACA 58.956 30.769 0.00 0.00 0.00 4.17
2179 4797 6.607735 AAAACAATGCAATCTTTTCCACAG 57.392 33.333 0.00 0.00 0.00 3.66
2180 4798 5.534207 AACAATGCAATCTTTTCCACAGA 57.466 34.783 0.00 0.00 0.00 3.41
2181 4799 5.733620 ACAATGCAATCTTTTCCACAGAT 57.266 34.783 0.00 0.00 31.94 2.90
2182 4800 5.717119 ACAATGCAATCTTTTCCACAGATC 58.283 37.500 0.00 0.00 30.19 2.75
2183 4801 4.996788 ATGCAATCTTTTCCACAGATCC 57.003 40.909 0.00 0.00 30.19 3.36
2184 4802 4.038271 TGCAATCTTTTCCACAGATCCT 57.962 40.909 0.00 0.00 30.19 3.24
2185 4803 5.178096 TGCAATCTTTTCCACAGATCCTA 57.822 39.130 0.00 0.00 30.19 2.94
2186 4804 5.569355 TGCAATCTTTTCCACAGATCCTAA 58.431 37.500 0.00 0.00 30.19 2.69
2187 4805 6.009589 TGCAATCTTTTCCACAGATCCTAAA 58.990 36.000 0.00 0.00 30.19 1.85
2188 4806 6.493115 TGCAATCTTTTCCACAGATCCTAAAA 59.507 34.615 0.00 0.00 30.19 1.52
2189 4807 7.178983 TGCAATCTTTTCCACAGATCCTAAAAT 59.821 33.333 0.00 0.00 30.19 1.82
2190 4808 7.704047 GCAATCTTTTCCACAGATCCTAAAATC 59.296 37.037 0.00 0.00 30.19 2.17
2191 4809 6.985188 TCTTTTCCACAGATCCTAAAATCG 57.015 37.500 0.00 0.00 0.00 3.34
2192 4810 5.880332 TCTTTTCCACAGATCCTAAAATCGG 59.120 40.000 0.00 0.00 0.00 4.18
2193 4811 3.838244 TCCACAGATCCTAAAATCGGG 57.162 47.619 0.00 0.00 0.00 5.14
2194 4812 3.112263 TCCACAGATCCTAAAATCGGGT 58.888 45.455 0.00 0.00 0.00 5.28
2195 4813 3.134081 TCCACAGATCCTAAAATCGGGTC 59.866 47.826 0.00 0.00 31.60 4.46
2196 4814 3.123804 CACAGATCCTAAAATCGGGTCG 58.876 50.000 0.00 0.00 36.76 4.79
2197 4815 2.102588 ACAGATCCTAAAATCGGGTCGG 59.897 50.000 0.00 0.00 36.76 4.79
2198 4816 1.070289 AGATCCTAAAATCGGGTCGGC 59.930 52.381 0.00 0.00 36.76 5.54
2199 4817 0.834612 ATCCTAAAATCGGGTCGGCA 59.165 50.000 0.00 0.00 0.00 5.69
2200 4818 0.177141 TCCTAAAATCGGGTCGGCAG 59.823 55.000 0.00 0.00 0.00 4.85
2201 4819 1.436983 CCTAAAATCGGGTCGGCAGC 61.437 60.000 0.00 0.00 0.00 5.25
2202 4820 0.462047 CTAAAATCGGGTCGGCAGCT 60.462 55.000 0.00 0.00 0.00 4.24
2203 4821 0.461339 TAAAATCGGGTCGGCAGCTC 60.461 55.000 0.00 0.00 0.00 4.09
2204 4822 2.185310 AAAATCGGGTCGGCAGCTCT 62.185 55.000 0.00 0.00 0.00 4.09
2205 4823 2.579684 AAATCGGGTCGGCAGCTCTC 62.580 60.000 0.00 0.00 0.00 3.20
2213 4831 4.567385 GGCAGCTCTCGCCTCTCG 62.567 72.222 6.31 0.00 46.56 4.04
2214 4832 4.567385 GCAGCTCTCGCCTCTCGG 62.567 72.222 0.00 0.00 39.05 4.63
2215 4833 3.137459 CAGCTCTCGCCTCTCGGT 61.137 66.667 0.00 0.00 39.05 4.69
2216 4834 3.137459 AGCTCTCGCCTCTCGGTG 61.137 66.667 0.00 0.00 42.32 4.94
2217 4835 3.444805 GCTCTCGCCTCTCGGTGT 61.445 66.667 0.00 0.00 41.65 4.16
2218 4836 2.795297 CTCTCGCCTCTCGGTGTC 59.205 66.667 0.00 0.00 41.65 3.67
2219 4837 3.102107 CTCTCGCCTCTCGGTGTCG 62.102 68.421 0.00 0.00 41.65 4.35
2220 4838 3.125573 CTCGCCTCTCGGTGTCGA 61.126 66.667 0.00 0.00 43.86 4.20
2221 4839 3.384014 CTCGCCTCTCGGTGTCGAC 62.384 68.421 9.11 9.11 40.88 4.20
2222 4840 4.477975 CGCCTCTCGGTGTCGACC 62.478 72.222 14.12 4.20 40.88 4.79
2232 4850 2.259505 GGTGTCGACCGAGACTAAAG 57.740 55.000 14.12 0.00 41.47 1.85
2233 4851 1.808945 GGTGTCGACCGAGACTAAAGA 59.191 52.381 14.12 0.00 41.47 2.52
2234 4852 2.227388 GGTGTCGACCGAGACTAAAGAA 59.773 50.000 14.12 0.00 41.47 2.52
2235 4853 3.304928 GGTGTCGACCGAGACTAAAGAAA 60.305 47.826 14.12 0.00 41.47 2.52
2236 4854 4.293415 GTGTCGACCGAGACTAAAGAAAA 58.707 43.478 14.12 0.00 41.47 2.29
2237 4855 4.741676 GTGTCGACCGAGACTAAAGAAAAA 59.258 41.667 14.12 0.00 41.47 1.94
2238 4856 4.741676 TGTCGACCGAGACTAAAGAAAAAC 59.258 41.667 14.12 0.00 41.47 2.43
2239 4857 4.741676 GTCGACCGAGACTAAAGAAAAACA 59.258 41.667 3.51 0.00 38.09 2.83
2240 4858 5.232838 GTCGACCGAGACTAAAGAAAAACAA 59.767 40.000 3.51 0.00 38.09 2.83
2241 4859 5.811613 TCGACCGAGACTAAAGAAAAACAAA 59.188 36.000 0.00 0.00 0.00 2.83
2242 4860 5.900242 CGACCGAGACTAAAGAAAAACAAAC 59.100 40.000 0.00 0.00 0.00 2.93
2243 4861 5.803118 ACCGAGACTAAAGAAAAACAAACG 58.197 37.500 0.00 0.00 0.00 3.60
2244 4862 5.202640 CCGAGACTAAAGAAAAACAAACGG 58.797 41.667 0.00 0.00 0.00 4.44
2245 4863 4.669283 CGAGACTAAAGAAAAACAAACGGC 59.331 41.667 0.00 0.00 0.00 5.68
2246 4864 4.594136 AGACTAAAGAAAAACAAACGGCG 58.406 39.130 4.80 4.80 0.00 6.46
2247 4865 3.697982 ACTAAAGAAAAACAAACGGCGG 58.302 40.909 13.24 0.00 0.00 6.13
2248 4866 2.943449 AAAGAAAAACAAACGGCGGA 57.057 40.000 13.24 0.00 0.00 5.54
2249 4867 2.485266 AAGAAAAACAAACGGCGGAG 57.515 45.000 13.24 2.48 0.00 4.63
2250 4868 1.670791 AGAAAAACAAACGGCGGAGA 58.329 45.000 13.24 0.00 0.00 3.71
2251 4869 1.332686 AGAAAAACAAACGGCGGAGAC 59.667 47.619 13.24 0.00 0.00 3.36
2252 4870 1.332686 GAAAAACAAACGGCGGAGACT 59.667 47.619 13.24 0.00 0.00 3.24
2253 4871 1.385528 AAAACAAACGGCGGAGACTT 58.614 45.000 13.24 0.00 0.00 3.01
2254 4872 2.243602 AAACAAACGGCGGAGACTTA 57.756 45.000 13.24 0.00 0.00 2.24
2255 4873 1.792006 AACAAACGGCGGAGACTTAG 58.208 50.000 13.24 0.00 0.00 2.18
2256 4874 0.669625 ACAAACGGCGGAGACTTAGC 60.670 55.000 13.24 0.00 0.00 3.09
2257 4875 0.669318 CAAACGGCGGAGACTTAGCA 60.669 55.000 13.24 0.00 0.00 3.49
2258 4876 0.034337 AAACGGCGGAGACTTAGCAA 59.966 50.000 13.24 0.00 0.00 3.91
2259 4877 0.249398 AACGGCGGAGACTTAGCAAT 59.751 50.000 13.24 0.00 0.00 3.56
2260 4878 1.108776 ACGGCGGAGACTTAGCAATA 58.891 50.000 13.24 0.00 0.00 1.90
2261 4879 1.202382 ACGGCGGAGACTTAGCAATAC 60.202 52.381 13.24 0.00 0.00 1.89
2262 4880 1.202371 CGGCGGAGACTTAGCAATACA 60.202 52.381 0.00 0.00 0.00 2.29
2263 4881 2.202566 GGCGGAGACTTAGCAATACAC 58.797 52.381 5.64 0.00 0.00 2.90
2264 4882 2.418197 GGCGGAGACTTAGCAATACACA 60.418 50.000 5.64 0.00 0.00 3.72
2265 4883 3.458189 GCGGAGACTTAGCAATACACAT 58.542 45.455 0.00 0.00 0.00 3.21
2266 4884 3.871594 GCGGAGACTTAGCAATACACATT 59.128 43.478 0.00 0.00 0.00 2.71
2267 4885 4.332819 GCGGAGACTTAGCAATACACATTT 59.667 41.667 0.00 0.00 0.00 2.32
2268 4886 5.502544 GCGGAGACTTAGCAATACACATTTC 60.503 44.000 0.00 0.00 0.00 2.17
2269 4887 5.006746 CGGAGACTTAGCAATACACATTTCC 59.993 44.000 0.00 0.00 0.00 3.13
2270 4888 6.116126 GGAGACTTAGCAATACACATTTCCT 58.884 40.000 0.00 0.00 0.00 3.36
2271 4889 6.599638 GGAGACTTAGCAATACACATTTCCTT 59.400 38.462 0.00 0.00 0.00 3.36
2272 4890 7.121315 GGAGACTTAGCAATACACATTTCCTTT 59.879 37.037 0.00 0.00 0.00 3.11
2273 4891 8.409358 AGACTTAGCAATACACATTTCCTTTT 57.591 30.769 0.00 0.00 0.00 2.27
2274 4892 9.515226 AGACTTAGCAATACACATTTCCTTTTA 57.485 29.630 0.00 0.00 0.00 1.52
2280 4898 9.995003 AGCAATACACATTTCCTTTTATTTGAA 57.005 25.926 0.00 0.00 0.00 2.69
2298 4916 9.555727 TTATTTGAAAGTTAGACAGTTAGTGCT 57.444 29.630 0.00 0.00 0.00 4.40
2299 4917 7.859325 TTTGAAAGTTAGACAGTTAGTGCTT 57.141 32.000 0.00 0.00 0.00 3.91
2300 4918 8.951787 TTTGAAAGTTAGACAGTTAGTGCTTA 57.048 30.769 0.00 0.00 0.00 3.09
2301 4919 9.555727 TTTGAAAGTTAGACAGTTAGTGCTTAT 57.444 29.630 0.00 0.00 0.00 1.73
2313 4931 9.099454 ACAGTTAGTGCTTATATGTTTCTTAGC 57.901 33.333 0.00 0.00 0.00 3.09
2314 4932 9.319143 CAGTTAGTGCTTATATGTTTCTTAGCT 57.681 33.333 0.00 0.00 0.00 3.32
2315 4933 9.892130 AGTTAGTGCTTATATGTTTCTTAGCTT 57.108 29.630 0.00 0.00 0.00 3.74
2316 4934 9.922305 GTTAGTGCTTATATGTTTCTTAGCTTG 57.078 33.333 0.00 0.00 0.00 4.01
2317 4935 7.020914 AGTGCTTATATGTTTCTTAGCTTGC 57.979 36.000 0.00 0.00 0.00 4.01
2318 4936 6.599244 AGTGCTTATATGTTTCTTAGCTTGCA 59.401 34.615 0.00 0.00 0.00 4.08
2319 4937 7.284034 AGTGCTTATATGTTTCTTAGCTTGCAT 59.716 33.333 0.00 0.00 0.00 3.96
2320 4938 7.917505 GTGCTTATATGTTTCTTAGCTTGCATT 59.082 33.333 0.00 0.00 0.00 3.56
2321 4939 8.469200 TGCTTATATGTTTCTTAGCTTGCATTT 58.531 29.630 0.00 0.00 0.00 2.32
2322 4940 9.305925 GCTTATATGTTTCTTAGCTTGCATTTT 57.694 29.630 0.00 0.00 0.00 1.82
2324 4942 5.851047 ATGTTTCTTAGCTTGCATTTTGC 57.149 34.783 0.00 0.00 45.29 3.68
2347 4965 5.868257 CGCTAAGCAAGAATTTATGTGACA 58.132 37.500 0.00 0.00 0.00 3.58
2348 4966 6.489675 CGCTAAGCAAGAATTTATGTGACAT 58.510 36.000 2.65 2.65 0.00 3.06
2349 4967 6.968904 CGCTAAGCAAGAATTTATGTGACATT 59.031 34.615 2.29 0.00 0.00 2.71
2350 4968 7.044510 CGCTAAGCAAGAATTTATGTGACATTG 60.045 37.037 2.29 0.00 0.00 2.82
2351 4969 6.956299 AAGCAAGAATTTATGTGACATTGC 57.044 33.333 2.29 6.54 41.50 3.56
2352 4970 5.097529 AGCAAGAATTTATGTGACATTGCG 58.902 37.500 2.29 0.00 44.80 4.85
2353 4971 5.094812 GCAAGAATTTATGTGACATTGCGA 58.905 37.500 2.29 0.00 33.35 5.10
2354 4972 5.003778 GCAAGAATTTATGTGACATTGCGAC 59.996 40.000 2.29 0.00 33.35 5.19
2355 4973 6.317088 CAAGAATTTATGTGACATTGCGACT 58.683 36.000 2.29 0.00 0.00 4.18
2356 4974 5.872635 AGAATTTATGTGACATTGCGACTG 58.127 37.500 2.29 0.00 0.00 3.51
2357 4975 5.412594 AGAATTTATGTGACATTGCGACTGT 59.587 36.000 2.29 0.00 0.00 3.55
2358 4976 4.403015 TTTATGTGACATTGCGACTGTG 57.597 40.909 2.29 0.00 0.00 3.66
2359 4977 2.168326 ATGTGACATTGCGACTGTGA 57.832 45.000 0.00 0.00 0.00 3.58
2360 4978 1.217001 TGTGACATTGCGACTGTGAC 58.783 50.000 0.00 0.00 32.26 3.67
2361 4979 1.217001 GTGACATTGCGACTGTGACA 58.783 50.000 0.00 0.00 31.98 3.58
2362 4980 1.800586 GTGACATTGCGACTGTGACAT 59.199 47.619 0.00 0.00 31.98 3.06
2363 4981 2.993220 GTGACATTGCGACTGTGACATA 59.007 45.455 0.00 0.00 31.98 2.29
2364 4982 3.431912 GTGACATTGCGACTGTGACATAA 59.568 43.478 0.00 0.00 31.98 1.90
2365 4983 3.679502 TGACATTGCGACTGTGACATAAG 59.320 43.478 0.00 0.00 0.00 1.73
2366 4984 3.925379 ACATTGCGACTGTGACATAAGA 58.075 40.909 0.00 0.00 0.00 2.10
2367 4985 3.928992 ACATTGCGACTGTGACATAAGAG 59.071 43.478 0.00 0.00 0.00 2.85
2368 4986 1.996292 TGCGACTGTGACATAAGAGC 58.004 50.000 0.00 0.00 0.00 4.09
2369 4987 1.272212 TGCGACTGTGACATAAGAGCA 59.728 47.619 0.00 9.83 0.00 4.26
2370 4988 2.094026 TGCGACTGTGACATAAGAGCAT 60.094 45.455 0.00 0.00 0.00 3.79
2371 4989 2.537625 GCGACTGTGACATAAGAGCATC 59.462 50.000 0.00 0.00 0.00 3.91
2387 5005 5.799827 GAGCATCTACAACTAAGGGATCT 57.200 43.478 0.00 0.00 0.00 2.75
2388 5006 6.902771 GAGCATCTACAACTAAGGGATCTA 57.097 41.667 0.00 0.00 0.00 1.98
2389 5007 6.909550 AGCATCTACAACTAAGGGATCTAG 57.090 41.667 0.00 0.00 0.00 2.43
2390 5008 6.377912 AGCATCTACAACTAAGGGATCTAGT 58.622 40.000 0.00 0.00 0.00 2.57
2391 5009 6.492087 AGCATCTACAACTAAGGGATCTAGTC 59.508 42.308 0.00 0.00 0.00 2.59
2392 5010 6.492087 GCATCTACAACTAAGGGATCTAGTCT 59.508 42.308 0.00 0.00 0.00 3.24
2393 5011 7.666388 GCATCTACAACTAAGGGATCTAGTCTA 59.334 40.741 0.00 0.00 0.00 2.59
2394 5012 9.005777 CATCTACAACTAAGGGATCTAGTCTAC 57.994 40.741 0.00 0.00 0.00 2.59
2395 5013 8.334522 TCTACAACTAAGGGATCTAGTCTACT 57.665 38.462 0.00 0.00 0.00 2.57
2396 5014 9.444668 TCTACAACTAAGGGATCTAGTCTACTA 57.555 37.037 0.00 0.00 0.00 1.82
2397 5015 9.715121 CTACAACTAAGGGATCTAGTCTACTAG 57.285 40.741 10.35 10.35 45.57 2.57
2409 5027 6.740411 CTAGTCTACTAGAACACGTTCCTT 57.260 41.667 11.03 0.00 46.80 3.36
2410 5028 7.840342 CTAGTCTACTAGAACACGTTCCTTA 57.160 40.000 11.03 0.00 46.80 2.69
2411 5029 8.436046 CTAGTCTACTAGAACACGTTCCTTAT 57.564 38.462 11.03 0.00 46.80 1.73
2412 5030 7.700022 AGTCTACTAGAACACGTTCCTTATT 57.300 36.000 6.30 0.00 40.33 1.40
2413 5031 8.798859 AGTCTACTAGAACACGTTCCTTATTA 57.201 34.615 6.30 0.00 40.33 0.98
2414 5032 9.406113 AGTCTACTAGAACACGTTCCTTATTAT 57.594 33.333 6.30 0.00 40.33 1.28
2422 5040 9.847224 AGAACACGTTCCTTATTATAATTCCAT 57.153 29.630 2.68 0.00 40.33 3.41
2449 5067 5.933187 AATAGTGTGCGTAAATGTTCACA 57.067 34.783 0.00 0.00 37.14 3.58
2450 5068 5.933187 ATAGTGTGCGTAAATGTTCACAA 57.067 34.783 0.00 0.00 40.57 3.33
2451 5069 4.624336 AGTGTGCGTAAATGTTCACAAA 57.376 36.364 0.00 0.00 40.57 2.83
2452 5070 4.347813 AGTGTGCGTAAATGTTCACAAAC 58.652 39.130 0.00 0.00 40.57 2.93
2453 5071 3.176867 GTGTGCGTAAATGTTCACAAACG 59.823 43.478 7.92 7.92 40.57 3.60
2454 5072 2.717011 GTGCGTAAATGTTCACAAACGG 59.283 45.455 12.12 0.00 38.28 4.44
2455 5073 1.711824 GCGTAAATGTTCACAAACGGC 59.288 47.619 12.12 4.47 38.28 5.68
2456 5074 1.966563 CGTAAATGTTCACAAACGGCG 59.033 47.619 4.80 4.80 38.28 6.46
2457 5075 2.348685 CGTAAATGTTCACAAACGGCGA 60.349 45.455 16.62 0.00 38.28 5.54
2458 5076 2.399396 AAATGTTCACAAACGGCGAG 57.601 45.000 16.62 5.45 38.28 5.03
2459 5077 1.588674 AATGTTCACAAACGGCGAGA 58.411 45.000 16.62 0.00 38.28 4.04
2460 5078 1.148310 ATGTTCACAAACGGCGAGAG 58.852 50.000 16.62 4.62 38.28 3.20
2461 5079 1.495584 TGTTCACAAACGGCGAGAGC 61.496 55.000 16.62 5.97 44.31 4.09
2545 5164 2.592993 CCACCGCTCCCCTTTCTCA 61.593 63.158 0.00 0.00 0.00 3.27
2557 5176 2.639839 CCCTTTCTCACCTTCCTTCTCA 59.360 50.000 0.00 0.00 0.00 3.27
2558 5177 3.307339 CCCTTTCTCACCTTCCTTCTCAG 60.307 52.174 0.00 0.00 0.00 3.35
2908 5584 4.344865 GGGCGGAGGTTGGCTTCA 62.345 66.667 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2122 4740 7.672660 TCCCTCTGTCTCATACTAGTGTAAAAA 59.327 37.037 5.39 0.00 31.80 1.94
2123 4741 7.179966 TCCCTCTGTCTCATACTAGTGTAAAA 58.820 38.462 5.39 0.00 31.80 1.52
2124 4742 6.728411 TCCCTCTGTCTCATACTAGTGTAAA 58.272 40.000 5.39 0.00 31.80 2.01
2125 4743 6.069556 ACTCCCTCTGTCTCATACTAGTGTAA 60.070 42.308 5.39 0.00 31.80 2.41
2126 4744 5.429109 ACTCCCTCTGTCTCATACTAGTGTA 59.571 44.000 5.39 0.00 0.00 2.90
2127 4745 4.228666 ACTCCCTCTGTCTCATACTAGTGT 59.771 45.833 5.39 0.00 0.00 3.55
2128 4746 4.787551 ACTCCCTCTGTCTCATACTAGTG 58.212 47.826 5.39 0.00 0.00 2.74
2129 4747 5.668535 AGTACTCCCTCTGTCTCATACTAGT 59.331 44.000 0.00 0.00 0.00 2.57
2130 4748 5.995282 CAGTACTCCCTCTGTCTCATACTAG 59.005 48.000 0.00 0.00 0.00 2.57
2131 4749 5.429109 ACAGTACTCCCTCTGTCTCATACTA 59.571 44.000 0.00 0.00 40.28 1.82
2132 4750 4.228666 ACAGTACTCCCTCTGTCTCATACT 59.771 45.833 0.00 0.00 40.28 2.12
2133 4751 4.528920 ACAGTACTCCCTCTGTCTCATAC 58.471 47.826 0.00 0.00 40.28 2.39
2134 4752 4.864483 ACAGTACTCCCTCTGTCTCATA 57.136 45.455 0.00 0.00 40.28 2.15
2135 4753 3.748645 ACAGTACTCCCTCTGTCTCAT 57.251 47.619 0.00 0.00 40.28 2.90
2136 4754 4.652679 TTACAGTACTCCCTCTGTCTCA 57.347 45.455 0.00 0.00 42.77 3.27
2137 4755 5.243283 TGTTTTACAGTACTCCCTCTGTCTC 59.757 44.000 0.00 0.00 42.77 3.36
2138 4756 5.145564 TGTTTTACAGTACTCCCTCTGTCT 58.854 41.667 0.00 0.00 42.77 3.41
2139 4757 5.464030 TGTTTTACAGTACTCCCTCTGTC 57.536 43.478 0.00 0.00 42.77 3.51
2140 4758 5.881923 TTGTTTTACAGTACTCCCTCTGT 57.118 39.130 0.00 0.00 45.21 3.41
2141 4759 5.122396 GCATTGTTTTACAGTACTCCCTCTG 59.878 44.000 0.00 0.00 37.65 3.35
2142 4760 5.221843 TGCATTGTTTTACAGTACTCCCTCT 60.222 40.000 0.00 0.00 0.00 3.69
2143 4761 5.001232 TGCATTGTTTTACAGTACTCCCTC 58.999 41.667 0.00 0.00 0.00 4.30
2144 4762 4.980573 TGCATTGTTTTACAGTACTCCCT 58.019 39.130 0.00 0.00 0.00 4.20
2145 4763 5.699097 TTGCATTGTTTTACAGTACTCCC 57.301 39.130 0.00 0.00 0.00 4.30
2146 4764 7.145932 AGATTGCATTGTTTTACAGTACTCC 57.854 36.000 0.00 0.00 0.00 3.85
2147 4765 9.463443 AAAAGATTGCATTGTTTTACAGTACTC 57.537 29.630 13.03 0.00 0.00 2.59
2148 4766 9.463443 GAAAAGATTGCATTGTTTTACAGTACT 57.537 29.630 14.24 0.00 0.00 2.73
2149 4767 8.699749 GGAAAAGATTGCATTGTTTTACAGTAC 58.300 33.333 16.96 5.77 0.00 2.73
2150 4768 8.417106 TGGAAAAGATTGCATTGTTTTACAGTA 58.583 29.630 19.41 3.67 29.61 2.74
2151 4769 7.224557 GTGGAAAAGATTGCATTGTTTTACAGT 59.775 33.333 22.27 1.76 39.21 3.55
2152 4770 7.224362 TGTGGAAAAGATTGCATTGTTTTACAG 59.776 33.333 22.27 0.00 39.21 2.74
2153 4771 7.044181 TGTGGAAAAGATTGCATTGTTTTACA 58.956 30.769 19.41 19.41 39.21 2.41
2154 4772 7.437862 TCTGTGGAAAAGATTGCATTGTTTTAC 59.562 33.333 15.64 15.64 39.21 2.01
2155 4773 7.495901 TCTGTGGAAAAGATTGCATTGTTTTA 58.504 30.769 14.24 0.84 39.21 1.52
2156 4774 6.347696 TCTGTGGAAAAGATTGCATTGTTTT 58.652 32.000 14.18 14.18 39.21 2.43
2157 4775 5.916318 TCTGTGGAAAAGATTGCATTGTTT 58.084 33.333 0.00 0.00 39.21 2.83
2158 4776 5.534207 TCTGTGGAAAAGATTGCATTGTT 57.466 34.783 0.00 0.00 39.21 2.83
2159 4777 5.337009 GGATCTGTGGAAAAGATTGCATTGT 60.337 40.000 0.00 0.00 42.24 2.71
2160 4778 5.105473 AGGATCTGTGGAAAAGATTGCATTG 60.105 40.000 0.00 0.00 42.24 2.82
2161 4779 5.021458 AGGATCTGTGGAAAAGATTGCATT 58.979 37.500 0.00 0.00 42.24 3.56
2162 4780 4.607239 AGGATCTGTGGAAAAGATTGCAT 58.393 39.130 0.00 0.00 42.24 3.96
2163 4781 4.038271 AGGATCTGTGGAAAAGATTGCA 57.962 40.909 0.00 0.00 42.24 4.08
2164 4782 6.515272 TTTAGGATCTGTGGAAAAGATTGC 57.485 37.500 0.00 0.00 42.24 3.56
2165 4783 7.912250 CGATTTTAGGATCTGTGGAAAAGATTG 59.088 37.037 0.00 0.00 42.24 2.67
2166 4784 7.067494 CCGATTTTAGGATCTGTGGAAAAGATT 59.933 37.037 0.00 0.00 42.24 2.40
2167 4785 6.543831 CCGATTTTAGGATCTGTGGAAAAGAT 59.456 38.462 0.00 0.00 45.77 2.40
2168 4786 5.880332 CCGATTTTAGGATCTGTGGAAAAGA 59.120 40.000 0.00 0.00 32.39 2.52
2169 4787 5.066505 CCCGATTTTAGGATCTGTGGAAAAG 59.933 44.000 0.00 0.00 0.00 2.27
2170 4788 4.947388 CCCGATTTTAGGATCTGTGGAAAA 59.053 41.667 0.00 0.00 0.00 2.29
2171 4789 4.018779 ACCCGATTTTAGGATCTGTGGAAA 60.019 41.667 0.00 0.00 0.00 3.13
2172 4790 3.521937 ACCCGATTTTAGGATCTGTGGAA 59.478 43.478 0.00 0.00 0.00 3.53
2173 4791 3.112263 ACCCGATTTTAGGATCTGTGGA 58.888 45.455 0.00 0.00 0.00 4.02
2174 4792 3.467803 GACCCGATTTTAGGATCTGTGG 58.532 50.000 0.00 0.00 0.00 4.17
2175 4793 3.123804 CGACCCGATTTTAGGATCTGTG 58.876 50.000 0.00 0.00 0.00 3.66
2176 4794 2.102588 CCGACCCGATTTTAGGATCTGT 59.897 50.000 0.00 0.00 0.00 3.41
2177 4795 2.755650 CCGACCCGATTTTAGGATCTG 58.244 52.381 0.00 0.00 0.00 2.90
2178 4796 1.070289 GCCGACCCGATTTTAGGATCT 59.930 52.381 0.00 0.00 0.00 2.75
2179 4797 1.202604 TGCCGACCCGATTTTAGGATC 60.203 52.381 0.00 0.00 0.00 3.36
2180 4798 0.834612 TGCCGACCCGATTTTAGGAT 59.165 50.000 0.00 0.00 0.00 3.24
2181 4799 0.177141 CTGCCGACCCGATTTTAGGA 59.823 55.000 0.00 0.00 0.00 2.94
2182 4800 1.436983 GCTGCCGACCCGATTTTAGG 61.437 60.000 0.00 0.00 0.00 2.69
2183 4801 0.462047 AGCTGCCGACCCGATTTTAG 60.462 55.000 0.00 0.00 0.00 1.85
2184 4802 0.461339 GAGCTGCCGACCCGATTTTA 60.461 55.000 0.00 0.00 0.00 1.52
2185 4803 1.745489 GAGCTGCCGACCCGATTTT 60.745 57.895 0.00 0.00 0.00 1.82
2186 4804 2.125106 GAGCTGCCGACCCGATTT 60.125 61.111 0.00 0.00 0.00 2.17
2187 4805 3.077556 AGAGCTGCCGACCCGATT 61.078 61.111 0.00 0.00 0.00 3.34
2188 4806 3.532155 GAGAGCTGCCGACCCGAT 61.532 66.667 0.00 0.00 0.00 4.18
2213 4831 1.808945 TCTTTAGTCTCGGTCGACACC 59.191 52.381 18.91 0.00 39.69 4.16
2214 4832 3.549299 TTCTTTAGTCTCGGTCGACAC 57.451 47.619 18.91 6.78 36.38 3.67
2215 4833 4.572985 TTTTCTTTAGTCTCGGTCGACA 57.427 40.909 18.91 0.00 36.38 4.35
2216 4834 4.741676 TGTTTTTCTTTAGTCTCGGTCGAC 59.258 41.667 7.13 7.13 0.00 4.20
2217 4835 4.935702 TGTTTTTCTTTAGTCTCGGTCGA 58.064 39.130 0.00 0.00 0.00 4.20
2218 4836 5.646467 TTGTTTTTCTTTAGTCTCGGTCG 57.354 39.130 0.00 0.00 0.00 4.79
2219 4837 5.900242 CGTTTGTTTTTCTTTAGTCTCGGTC 59.100 40.000 0.00 0.00 0.00 4.79
2220 4838 5.220719 CCGTTTGTTTTTCTTTAGTCTCGGT 60.221 40.000 0.00 0.00 0.00 4.69
2221 4839 5.202640 CCGTTTGTTTTTCTTTAGTCTCGG 58.797 41.667 0.00 0.00 0.00 4.63
2222 4840 4.669283 GCCGTTTGTTTTTCTTTAGTCTCG 59.331 41.667 0.00 0.00 0.00 4.04
2223 4841 4.669283 CGCCGTTTGTTTTTCTTTAGTCTC 59.331 41.667 0.00 0.00 0.00 3.36
2224 4842 4.496840 CCGCCGTTTGTTTTTCTTTAGTCT 60.497 41.667 0.00 0.00 0.00 3.24
2225 4843 3.727227 CCGCCGTTTGTTTTTCTTTAGTC 59.273 43.478 0.00 0.00 0.00 2.59
2226 4844 3.377798 TCCGCCGTTTGTTTTTCTTTAGT 59.622 39.130 0.00 0.00 0.00 2.24
2227 4845 3.954999 TCCGCCGTTTGTTTTTCTTTAG 58.045 40.909 0.00 0.00 0.00 1.85
2228 4846 3.626670 TCTCCGCCGTTTGTTTTTCTTTA 59.373 39.130 0.00 0.00 0.00 1.85
2229 4847 2.424246 TCTCCGCCGTTTGTTTTTCTTT 59.576 40.909 0.00 0.00 0.00 2.52
2230 4848 2.018515 TCTCCGCCGTTTGTTTTTCTT 58.981 42.857 0.00 0.00 0.00 2.52
2231 4849 1.332686 GTCTCCGCCGTTTGTTTTTCT 59.667 47.619 0.00 0.00 0.00 2.52
2232 4850 1.332686 AGTCTCCGCCGTTTGTTTTTC 59.667 47.619 0.00 0.00 0.00 2.29
2233 4851 1.385528 AGTCTCCGCCGTTTGTTTTT 58.614 45.000 0.00 0.00 0.00 1.94
2234 4852 1.385528 AAGTCTCCGCCGTTTGTTTT 58.614 45.000 0.00 0.00 0.00 2.43
2235 4853 2.140717 CTAAGTCTCCGCCGTTTGTTT 58.859 47.619 0.00 0.00 0.00 2.83
2236 4854 1.792006 CTAAGTCTCCGCCGTTTGTT 58.208 50.000 0.00 0.00 0.00 2.83
2237 4855 0.669625 GCTAAGTCTCCGCCGTTTGT 60.670 55.000 0.00 0.00 0.00 2.83
2238 4856 0.669318 TGCTAAGTCTCCGCCGTTTG 60.669 55.000 0.00 0.00 0.00 2.93
2239 4857 0.034337 TTGCTAAGTCTCCGCCGTTT 59.966 50.000 0.00 0.00 0.00 3.60
2240 4858 0.249398 ATTGCTAAGTCTCCGCCGTT 59.751 50.000 0.00 0.00 0.00 4.44
2241 4859 1.108776 TATTGCTAAGTCTCCGCCGT 58.891 50.000 0.00 0.00 0.00 5.68
2242 4860 1.202371 TGTATTGCTAAGTCTCCGCCG 60.202 52.381 0.00 0.00 0.00 6.46
2243 4861 2.202566 GTGTATTGCTAAGTCTCCGCC 58.797 52.381 0.00 0.00 0.00 6.13
2244 4862 2.888594 TGTGTATTGCTAAGTCTCCGC 58.111 47.619 0.00 0.00 0.00 5.54
2245 4863 5.006746 GGAAATGTGTATTGCTAAGTCTCCG 59.993 44.000 0.00 0.00 0.00 4.63
2246 4864 6.116126 AGGAAATGTGTATTGCTAAGTCTCC 58.884 40.000 0.00 0.00 0.00 3.71
2247 4865 7.617041 AAGGAAATGTGTATTGCTAAGTCTC 57.383 36.000 0.00 0.00 0.00 3.36
2248 4866 8.409358 AAAAGGAAATGTGTATTGCTAAGTCT 57.591 30.769 0.00 0.00 0.00 3.24
2254 4872 9.995003 TTCAAATAAAAGGAAATGTGTATTGCT 57.005 25.926 0.00 0.00 0.00 3.91
2272 4890 9.555727 AGCACTAACTGTCTAACTTTCAAATAA 57.444 29.630 0.00 0.00 0.00 1.40
2273 4891 9.555727 AAGCACTAACTGTCTAACTTTCAAATA 57.444 29.630 0.00 0.00 0.00 1.40
2274 4892 8.451908 AAGCACTAACTGTCTAACTTTCAAAT 57.548 30.769 0.00 0.00 0.00 2.32
2275 4893 7.859325 AAGCACTAACTGTCTAACTTTCAAA 57.141 32.000 0.00 0.00 0.00 2.69
2287 4905 9.099454 GCTAAGAAACATATAAGCACTAACTGT 57.901 33.333 0.00 0.00 0.00 3.55
2288 4906 9.319143 AGCTAAGAAACATATAAGCACTAACTG 57.681 33.333 0.00 0.00 32.42 3.16
2289 4907 9.892130 AAGCTAAGAAACATATAAGCACTAACT 57.108 29.630 0.00 0.00 32.42 2.24
2290 4908 9.922305 CAAGCTAAGAAACATATAAGCACTAAC 57.078 33.333 0.00 0.00 32.42 2.34
2291 4909 8.612619 GCAAGCTAAGAAACATATAAGCACTAA 58.387 33.333 0.00 0.00 32.42 2.24
2292 4910 7.768582 TGCAAGCTAAGAAACATATAAGCACTA 59.231 33.333 0.00 0.00 32.42 2.74
2293 4911 6.599244 TGCAAGCTAAGAAACATATAAGCACT 59.401 34.615 0.00 0.00 32.42 4.40
2294 4912 6.785191 TGCAAGCTAAGAAACATATAAGCAC 58.215 36.000 0.00 0.00 32.42 4.40
2295 4913 7.572523 ATGCAAGCTAAGAAACATATAAGCA 57.427 32.000 0.00 0.00 32.42 3.91
2296 4914 8.862550 AAATGCAAGCTAAGAAACATATAAGC 57.137 30.769 0.00 0.00 0.00 3.09
2298 4916 9.086336 GCAAAATGCAAGCTAAGAAACATATAA 57.914 29.630 0.00 0.00 44.26 0.98
2299 4917 7.431960 CGCAAAATGCAAGCTAAGAAACATATA 59.568 33.333 2.99 0.00 45.36 0.86
2300 4918 6.254157 CGCAAAATGCAAGCTAAGAAACATAT 59.746 34.615 2.99 0.00 45.36 1.78
2301 4919 5.572511 CGCAAAATGCAAGCTAAGAAACATA 59.427 36.000 2.99 0.00 45.36 2.29
2302 4920 4.386652 CGCAAAATGCAAGCTAAGAAACAT 59.613 37.500 2.99 0.00 45.36 2.71
2303 4921 3.735240 CGCAAAATGCAAGCTAAGAAACA 59.265 39.130 2.99 0.00 45.36 2.83
2304 4922 3.422214 GCGCAAAATGCAAGCTAAGAAAC 60.422 43.478 0.30 0.00 45.36 2.78
2305 4923 2.730928 GCGCAAAATGCAAGCTAAGAAA 59.269 40.909 0.30 0.00 45.36 2.52
2306 4924 2.030007 AGCGCAAAATGCAAGCTAAGAA 60.030 40.909 11.47 0.00 45.36 2.52
2307 4925 1.541147 AGCGCAAAATGCAAGCTAAGA 59.459 42.857 11.47 0.00 45.36 2.10
2308 4926 1.986698 AGCGCAAAATGCAAGCTAAG 58.013 45.000 11.47 0.00 45.36 2.18
2309 4927 3.500982 CTTAGCGCAAAATGCAAGCTAA 58.499 40.909 11.47 17.60 44.24 3.09
2310 4928 2.731968 GCTTAGCGCAAAATGCAAGCTA 60.732 45.455 11.47 11.36 45.36 3.32
2311 4929 1.986698 CTTAGCGCAAAATGCAAGCT 58.013 45.000 11.47 9.17 45.36 3.74
2312 4930 0.367887 GCTTAGCGCAAAATGCAAGC 59.632 50.000 11.47 8.58 45.36 4.01
2323 4941 4.730521 GTCACATAAATTCTTGCTTAGCGC 59.269 41.667 0.00 0.00 39.77 5.92
2324 4942 5.868257 TGTCACATAAATTCTTGCTTAGCG 58.132 37.500 0.00 0.00 0.00 4.26
2325 4943 7.253883 GCAATGTCACATAAATTCTTGCTTAGC 60.254 37.037 0.00 0.00 35.92 3.09
2326 4944 7.044510 CGCAATGTCACATAAATTCTTGCTTAG 60.045 37.037 8.08 0.00 36.49 2.18
2327 4945 6.746822 CGCAATGTCACATAAATTCTTGCTTA 59.253 34.615 8.08 0.00 36.49 3.09
2328 4946 5.574055 CGCAATGTCACATAAATTCTTGCTT 59.426 36.000 8.08 0.00 36.49 3.91
2329 4947 5.097529 CGCAATGTCACATAAATTCTTGCT 58.902 37.500 8.08 0.00 36.49 3.91
2330 4948 5.003778 GTCGCAATGTCACATAAATTCTTGC 59.996 40.000 0.00 0.00 35.58 4.01
2331 4949 6.249893 CAGTCGCAATGTCACATAAATTCTTG 59.750 38.462 0.00 0.00 0.00 3.02
2332 4950 6.072508 ACAGTCGCAATGTCACATAAATTCTT 60.073 34.615 0.00 0.00 0.00 2.52
2333 4951 5.412594 ACAGTCGCAATGTCACATAAATTCT 59.587 36.000 0.00 0.00 0.00 2.40
2334 4952 5.509272 CACAGTCGCAATGTCACATAAATTC 59.491 40.000 0.00 0.00 0.00 2.17
2335 4953 5.181056 TCACAGTCGCAATGTCACATAAATT 59.819 36.000 0.00 0.00 0.00 1.82
2336 4954 4.694982 TCACAGTCGCAATGTCACATAAAT 59.305 37.500 0.00 0.00 0.00 1.40
2337 4955 4.061596 TCACAGTCGCAATGTCACATAAA 58.938 39.130 0.00 0.00 0.00 1.40
2338 4956 3.431912 GTCACAGTCGCAATGTCACATAA 59.568 43.478 0.00 0.00 0.00 1.90
2339 4957 2.993220 GTCACAGTCGCAATGTCACATA 59.007 45.455 0.00 0.00 0.00 2.29
2340 4958 1.800586 GTCACAGTCGCAATGTCACAT 59.199 47.619 0.00 0.00 0.00 3.21
2341 4959 1.217001 GTCACAGTCGCAATGTCACA 58.783 50.000 0.00 0.00 0.00 3.58
2342 4960 1.217001 TGTCACAGTCGCAATGTCAC 58.783 50.000 0.00 0.00 0.00 3.67
2343 4961 2.168326 ATGTCACAGTCGCAATGTCA 57.832 45.000 0.00 0.00 0.00 3.58
2344 4962 3.926527 TCTTATGTCACAGTCGCAATGTC 59.073 43.478 0.00 0.00 0.00 3.06
2345 4963 3.925379 TCTTATGTCACAGTCGCAATGT 58.075 40.909 0.00 0.00 0.00 2.71
2346 4964 3.242220 GCTCTTATGTCACAGTCGCAATG 60.242 47.826 0.00 0.00 0.00 2.82
2347 4965 2.932614 GCTCTTATGTCACAGTCGCAAT 59.067 45.455 0.00 0.00 0.00 3.56
2348 4966 2.288763 TGCTCTTATGTCACAGTCGCAA 60.289 45.455 0.00 0.00 0.00 4.85
2349 4967 1.272212 TGCTCTTATGTCACAGTCGCA 59.728 47.619 0.00 0.00 0.00 5.10
2350 4968 1.996292 TGCTCTTATGTCACAGTCGC 58.004 50.000 0.00 0.00 0.00 5.19
2351 4969 4.039151 AGATGCTCTTATGTCACAGTCG 57.961 45.455 0.00 0.00 0.00 4.18
2352 4970 5.895928 TGTAGATGCTCTTATGTCACAGTC 58.104 41.667 0.00 0.00 0.00 3.51
2353 4971 5.921962 TGTAGATGCTCTTATGTCACAGT 57.078 39.130 0.00 0.00 0.00 3.55
2354 4972 6.336566 AGTTGTAGATGCTCTTATGTCACAG 58.663 40.000 0.00 0.00 0.00 3.66
2355 4973 6.286240 AGTTGTAGATGCTCTTATGTCACA 57.714 37.500 0.00 0.00 0.00 3.58
2356 4974 7.436673 CCTTAGTTGTAGATGCTCTTATGTCAC 59.563 40.741 0.00 0.00 0.00 3.67
2357 4975 7.417911 CCCTTAGTTGTAGATGCTCTTATGTCA 60.418 40.741 0.00 0.00 0.00 3.58
2358 4976 6.926272 CCCTTAGTTGTAGATGCTCTTATGTC 59.074 42.308 0.00 0.00 0.00 3.06
2359 4977 6.611642 TCCCTTAGTTGTAGATGCTCTTATGT 59.388 38.462 0.00 0.00 0.00 2.29
2360 4978 7.055667 TCCCTTAGTTGTAGATGCTCTTATG 57.944 40.000 0.00 0.00 0.00 1.90
2361 4979 7.732593 AGATCCCTTAGTTGTAGATGCTCTTAT 59.267 37.037 0.00 0.00 0.00 1.73
2362 4980 7.069986 AGATCCCTTAGTTGTAGATGCTCTTA 58.930 38.462 0.00 0.00 0.00 2.10
2363 4981 5.902431 AGATCCCTTAGTTGTAGATGCTCTT 59.098 40.000 0.00 0.00 0.00 2.85
2364 4982 5.463154 AGATCCCTTAGTTGTAGATGCTCT 58.537 41.667 0.00 0.00 0.00 4.09
2365 4983 5.799827 AGATCCCTTAGTTGTAGATGCTC 57.200 43.478 0.00 0.00 0.00 4.26
2366 4984 6.377912 ACTAGATCCCTTAGTTGTAGATGCT 58.622 40.000 0.00 0.00 0.00 3.79
2367 4985 6.492087 AGACTAGATCCCTTAGTTGTAGATGC 59.508 42.308 0.00 0.00 0.00 3.91
2368 4986 9.005777 GTAGACTAGATCCCTTAGTTGTAGATG 57.994 40.741 0.00 0.00 0.00 2.90
2369 4987 8.951541 AGTAGACTAGATCCCTTAGTTGTAGAT 58.048 37.037 0.00 0.00 0.00 1.98
2370 4988 8.334522 AGTAGACTAGATCCCTTAGTTGTAGA 57.665 38.462 0.00 0.00 0.00 2.59
2371 4989 9.715121 CTAGTAGACTAGATCCCTTAGTTGTAG 57.285 40.741 10.66 0.00 46.80 2.74
2386 5004 6.740411 AAGGAACGTGTTCTAGTAGACTAG 57.260 41.667 12.10 10.00 45.57 2.57
2387 5005 8.798859 AATAAGGAACGTGTTCTAGTAGACTA 57.201 34.615 12.10 0.00 39.45 2.59
2388 5006 7.700022 AATAAGGAACGTGTTCTAGTAGACT 57.300 36.000 12.10 0.00 39.45 3.24
2396 5014 9.847224 ATGGAATTATAATAAGGAACGTGTTCT 57.153 29.630 12.10 0.00 39.45 3.01
2423 5041 9.320352 TGTGAACATTTACGCACACTATTATAT 57.680 29.630 0.00 0.00 36.44 0.86
2424 5042 8.705048 TGTGAACATTTACGCACACTATTATA 57.295 30.769 0.00 0.00 36.44 0.98
2425 5043 7.603963 TGTGAACATTTACGCACACTATTAT 57.396 32.000 0.00 0.00 36.44 1.28
2426 5044 7.422878 TTGTGAACATTTACGCACACTATTA 57.577 32.000 0.00 0.00 40.57 0.98
2427 5045 5.933187 TGTGAACATTTACGCACACTATT 57.067 34.783 0.00 0.00 36.44 1.73
2428 5046 5.933187 TTGTGAACATTTACGCACACTAT 57.067 34.783 0.00 0.00 40.57 2.12
2429 5047 5.503498 GTTTGTGAACATTTACGCACACTA 58.497 37.500 0.00 0.00 40.57 2.74
2430 5048 4.347813 GTTTGTGAACATTTACGCACACT 58.652 39.130 0.00 0.00 40.57 3.55
2431 5049 3.176867 CGTTTGTGAACATTTACGCACAC 59.823 43.478 0.00 0.00 40.57 3.82
2432 5050 3.355270 CGTTTGTGAACATTTACGCACA 58.645 40.909 0.00 0.00 39.27 4.57
2433 5051 2.717011 CCGTTTGTGAACATTTACGCAC 59.283 45.455 0.00 0.00 35.44 5.34
2434 5052 2.855187 GCCGTTTGTGAACATTTACGCA 60.855 45.455 0.00 0.00 35.44 5.24
2435 5053 1.711824 GCCGTTTGTGAACATTTACGC 59.288 47.619 0.00 0.00 35.44 4.42
2436 5054 1.966563 CGCCGTTTGTGAACATTTACG 59.033 47.619 0.00 0.00 35.44 3.18
2437 5055 3.059461 TCTCGCCGTTTGTGAACATTTAC 60.059 43.478 0.00 0.00 35.44 2.01
2438 5056 3.132160 TCTCGCCGTTTGTGAACATTTA 58.868 40.909 0.00 0.00 35.44 1.40
2439 5057 1.944024 TCTCGCCGTTTGTGAACATTT 59.056 42.857 0.00 0.00 35.44 2.32
2440 5058 1.531149 CTCTCGCCGTTTGTGAACATT 59.469 47.619 0.00 0.00 35.44 2.71
2441 5059 1.148310 CTCTCGCCGTTTGTGAACAT 58.852 50.000 0.00 0.00 35.44 2.71
2442 5060 1.495584 GCTCTCGCCGTTTGTGAACA 61.496 55.000 0.00 0.00 35.44 3.18
2443 5061 1.204312 GCTCTCGCCGTTTGTGAAC 59.796 57.895 0.00 0.00 31.89 3.18
2444 5062 1.221466 CTGCTCTCGCCGTTTGTGAA 61.221 55.000 0.00 0.00 31.89 3.18
2445 5063 1.664649 CTGCTCTCGCCGTTTGTGA 60.665 57.895 0.00 0.00 34.43 3.58
2446 5064 1.221466 TTCTGCTCTCGCCGTTTGTG 61.221 55.000 0.00 0.00 34.43 3.33
2447 5065 1.069090 TTCTGCTCTCGCCGTTTGT 59.931 52.632 0.00 0.00 34.43 2.83
2448 5066 1.221466 TGTTCTGCTCTCGCCGTTTG 61.221 55.000 0.00 0.00 34.43 2.93
2449 5067 0.946221 CTGTTCTGCTCTCGCCGTTT 60.946 55.000 0.00 0.00 34.43 3.60
2450 5068 1.373497 CTGTTCTGCTCTCGCCGTT 60.373 57.895 0.00 0.00 34.43 4.44
2451 5069 2.206515 CTCTGTTCTGCTCTCGCCGT 62.207 60.000 0.00 0.00 34.43 5.68
2452 5070 1.515952 CTCTGTTCTGCTCTCGCCG 60.516 63.158 0.00 0.00 34.43 6.46
2453 5071 0.179140 CTCTCTGTTCTGCTCTCGCC 60.179 60.000 0.00 0.00 34.43 5.54
2454 5072 0.808125 TCTCTCTGTTCTGCTCTCGC 59.192 55.000 0.00 0.00 0.00 5.03
2455 5073 2.415357 GGTTCTCTCTGTTCTGCTCTCG 60.415 54.545 0.00 0.00 0.00 4.04
2456 5074 2.415357 CGGTTCTCTCTGTTCTGCTCTC 60.415 54.545 0.00 0.00 0.00 3.20
2457 5075 1.543802 CGGTTCTCTCTGTTCTGCTCT 59.456 52.381 0.00 0.00 0.00 4.09
2458 5076 1.271102 ACGGTTCTCTCTGTTCTGCTC 59.729 52.381 0.00 0.00 0.00 4.26
2459 5077 1.271102 GACGGTTCTCTCTGTTCTGCT 59.729 52.381 0.00 0.00 0.00 4.24
2460 5078 1.670380 GGACGGTTCTCTCTGTTCTGC 60.670 57.143 0.00 0.00 0.00 4.26
2461 5079 1.889829 AGGACGGTTCTCTCTGTTCTG 59.110 52.381 0.00 0.00 31.93 3.02
2462 5080 2.164338 GAGGACGGTTCTCTCTGTTCT 58.836 52.381 9.26 0.00 35.45 3.01
2463 5081 1.202817 GGAGGACGGTTCTCTCTGTTC 59.797 57.143 15.80 0.00 0.00 3.18
2464 5082 1.258676 GGAGGACGGTTCTCTCTGTT 58.741 55.000 15.80 0.00 0.00 3.16
2465 5083 0.961358 CGGAGGACGGTTCTCTCTGT 60.961 60.000 15.80 0.00 39.42 3.41
2466 5084 1.803943 CGGAGGACGGTTCTCTCTG 59.196 63.158 15.80 8.52 39.42 3.35
2467 5085 4.322689 CGGAGGACGGTTCTCTCT 57.677 61.111 15.80 0.00 39.42 3.10
2545 5164 1.878656 CGGCGACTGAGAAGGAAGGT 61.879 60.000 0.00 0.00 0.00 3.50
3039 5718 2.107750 CACGGCATCCAGATCGCT 59.892 61.111 0.00 0.00 0.00 4.93
3068 5756 1.069765 AATACCGGCAGATCAGCGG 59.930 57.895 15.68 15.68 35.37 5.52


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.